Support Nunjucks templating engine for API call construction

__test__/data/multi_input_edge.json

@@ -0,0 +1,76 @@
+{
+  "input": {
+    "id": "MONDO:0005252",
+    "fields": [
+      "subject",
+      "association"
+    ],
+    "specialpath": "/querytest"
+  },
+  "query_operation": {
+    "path_params": [
+      "path"
+    ],
+    "params": {
+      "fields": "{{ fields | join(',') }}",
+      "q": "object.MONDO:\"{{ id }}\" AND subject.type:SmallMolecule",
+      "size": 1000,
+      "path": "{{ specialpath }}"
+    },
+    "request_body": {
+      "body": {
+        "q": "{{ id }}",
+        "fields": "{{ fields | join(',') }}"
+      },
+      "header": "application/x-www-form-urlencoded"
+    },
+    "supportBatch": false,
+    "method": "get",
+    "pathParams": [],
+    "server": "https://biothings.ncats.io/text_mining_co_occurrence_kp",
+    "path": "{path}",
+    "tags": [
+      "gene",
+      "chemical",
+      "association",
+      "annotation",
+      "query",
+      "translator",
+      "biothings",
+      "biothings_graph"
+    ]
+  },
+  "association": {
+    "input_id": "MONDO",
+    "input_type": "Disease",
+    "output_id": "CHEBI",
+    "output_type": "SmallMolecule",
+    "predicate": "related_to",
+    "source": "Text Mining KP",
+    "api_name": "Text Mining CO-OCCURRENCE API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": [
+        "Text Mining Provider",
+        "Service Provider"
+      ]
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "CHEBI": "hits.subject.CHEBI",
+      "ngd": "hits.association.ngd"
+    }
+  },
+  "tags": [
+    "gene",
+    "chemical",
+    "association",
+    "annotation",
+    "query",
+    "translator",
+    "biothings",
+    "biothings_graph"
+  ]
+}

__test__/integration/integration.test.js

@@ -64,4 +64,4 @@ describe("Integration test", () => {
             expect(res.length).toEqual(mydisease_res.data["mondo.descendants"].length)
         })
     })
-})
+})

__test__/query_builder.test.js

@@ -3,6 +3,8 @@
  */
 
 const qb = require("../src/builder/query_builder");
+const path = require("path");
+const fs = require ("fs");
 
 describe("test query builder class", () => {
 
@@ -64,6 +66,15 @@ describe("test query builder class", () => {
             const res = builder._getUrl(edge, 'hello');
             expect(res).toBe("https://google.com/hello/json/query")
         })
+
+        test("if _getUrl nunjucks templates are filled", () => {
+            const edge_path = path.resolve(__dirname, "data/multi_input_edge.json");
+            edge = JSON.parse(fs.readFileSync(edge_path));
+
+            const builder = new qb(edge);
+            const res = builder._getUrl(edge, edge.input);
+            expect(res).toEqual("https://biothings.ncats.io/text_mining_co_occurrence_kp/querytest");
+        })
     })
 
     describe("Test _getInput function", () => {
@@ -175,6 +186,19 @@ describe("test query builder class", () => {
             const res = builder._getParams(edge, '1017');
             expect(res.output).toEqual(1);
         })
+
+        test("if _getParams nunjucks templates are filled", () => {
+            const edge_path = path.resolve(__dirname, "data/multi_input_edge.json");
+            edge = JSON.parse(fs.readFileSync(edge_path));
+
+            const builder = new qb(edge);
+            const res = builder._getParams(edge, edge.input);
+            expect(res).toEqual({
+              fields: "subject,association",
+              q: 'object.MONDO:"MONDO:0005252" AND subject.type:SmallMolecule',
+              size: 1000,
+            });
+        })
     })
 
     describe("test _getRequestBody function", () => {
@@ -230,6 +254,15 @@ describe("test query builder class", () => {
             const res = builder._getRequestBody(edge, "1017");
             expect(res).toEqual("geneid=hello&output=1017")
         })
+
+        test("if nunjucks _getRequestBody templates are filled", () => {
+            const edge_path = path.resolve(__dirname, "data/multi_input_edge.json");
+            edge = JSON.parse(fs.readFileSync(edge_path));
+
+            const builder = new qb(edge);
+            const res = builder._getRequestBody(edge, edge.input);
+            expect(res).toEqual("q=MONDO:0005252&fields=subject,association");
+        });
     })
 
     describe("test constructAxiosRequestConfig function", () => {
@@ -323,4 +356,4 @@ describe("test query builder class", () => {
             expect(res).toBeFalsy();
         })
     })
-})
+})

__test__/template_funcs.test.js

@@ -0,0 +1,101 @@
+const nunjucks = require("nunjucks");
+const nunjucksConfig = require("../src/builder/nunjucks_config");
+const env = nunjucks.configure({ autoescape: false });
+nunjucksConfig(env);
+
+describe("test templateFuncs", () => {
+
+  test("substr behavior", () => {
+    const str = "abcdefghi";
+    const run = (str, begin, end) => nunjucks.renderString(`{{ test | substr(${begin}, ${end}) }}`, {test: str});
+    let res;
+    res = run(str);
+    expect(res).toEqual(str);
+    res = run(str, 1);
+    expect(res).toEqual(str.slice(1));
+    res = run(str, 3, 6);
+    expect(res).toEqual(str.slice(3, 6));
+    res = run(str, 0, -3);
+    expect(res).toEqual(str.slice(0, -3));
+  });
+
+  test("addPrefix behavior", () => {
+    const has = "PREFIX:usefulid";
+    const hasnot = "usefulid";
+    const run = (str, prefix, delim) => {
+      prefix = typeof prefix === 'undefined' ? undefined : `"${prefix}"`;
+      delim = typeof delim === 'undefined' ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | addPrefix(${prefix}, ${delim}) }}`, {test: str})
+    };
+    let res;
+    res = run(hasnot, "PREFIX");
+    expect(res).toEqual(has);
+    res = run(hasnot, "PREFIX", "-");
+    expect(res).toEqual("PREFIX-" + hasnot);
+  });
+
+  test("rmPrefix behavior", () => {
+    const has = "PREFIX:usefulid";
+    const hasnot = "usefulid";
+    const run = (str, delim) => {
+      delim = typeof delim === 'undefined' ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | rmPrefix(${delim}) }}`, {test: str})
+    };
+    let res;
+    res = run(has);
+    expect(res).toEqual(hasnot);
+    res = run(has, "-");
+    expect(res).toEqual(has);
+    res = run(hasnot);
+    expect(res).toEqual(hasnot);
+  });
+
+  test("replPrefix behavior", () => {
+    const has = "PREFIX:usefulid";
+    const hasnot = "usefulid";
+    const run = (str, prefix, delim) => {
+      prefix = typeof prefix === 'undefined' ? undefined : `"${prefix}"`;
+      delim = typeof delim === 'undefined' ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | replPrefix(${prefix}, ${delim}) }}`, {test: str})
+    };
+    let res;
+    res = run(has, "NEWFIX");
+    expect(res).toEqual("NEWFIX:" + hasnot);
+    res = run(hasnot, "NEWFIX");
+    expect(res).toEqual("NEWFIX:" + hasnot);
+    res = run(has);
+    expect(res).toEqual(hasnot);
+    res = run(has, "NEWFIX", "-");
+    expect(res).toEqual("NEWFIX-PREFIX:" + hasnot);
+  });
+
+  test("array usage", () => {
+    const has = ["PREFIX:id0", "PREFIX:id1", "PREFIX:id2"];
+    const hasnot = "usefulid";
+    let res;
+    let run = (str, delim) => {
+      prefix = typeof prefix === "undefined" ? undefined : `"${prefix}"`;
+      delim = typeof delim === "undefined" ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | rmPrefix(${prefix}, ${delim}) | join(",") }}`, { test: str });
+    };
+    res = run(has);
+    expect(res).toEqual("id0,id1,id2");
+    run = (str, prefix, delim) => {
+      prefix = typeof prefix === "undefined" ? undefined : `"${prefix}"`;
+      delim = typeof delim === "undefined" ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | addPrefix(${prefix}, ${delim}) | join(",") }}`, { test: str });
+    };
+    res = run(has, "test", ":");
+    expect(res).toEqual('test:PREFIX:id0,test:PREFIX:id1,test:PREFIX:id2');
+    run = (str, prefix, delim) => {
+      prefix = typeof prefix === "undefined" ? undefined : `"${prefix}"`;
+      delim = typeof delim === "undefined" ? undefined : `"${delim}"`;
+      return nunjucks.renderString(`{{ test | replPrefix(${prefix}, ${delim}) | join(",") }}`, { test: str });
+    };
+    res = run(has, "test");
+    expect(res).toEqual("test:id0,test:id1,test:id2");
+    run = run = (str, begin, end) => nunjucks.renderString(`{{ test | substr(${begin}, ${end}) }}`, { test: str });
+    res = run(has, -3);
+    expect(res).toEqual("id0,id1,id2");
+  })
+});

__test__/trapi_query_builder.test.js

@@ -30,4 +30,68 @@ describe("test trapi query builder class", () => {
             expect(res.data.message.query_graph.edges.e01.predicates).toContain('biolink:related_to');
         })
     })
-})
+
+    describe("test nunjucks support", () => {
+        test("if _getUrl nunjucks templates are filled", () => {
+            const edge = {
+                query_operation: {
+                    server: "https://google.com/",
+                    path: "{path}",
+                    path_params: ["path"],
+                    params: {path: "{{ specialpath }}"}
+                },
+                association: {
+                    input_type: "Pathway",
+                    output_type: "Gene",
+                    predicate: "related_to",
+                },
+                input: {specialpath: "/querytest"},
+            };
+            const builder = new qb(edge);
+            const res = builder._getUrl(edge, edge.input);
+            expect(res).toEqual("https://google.com/querytest");
+        })
+
+        test("if _getBody nunjucks templates are filled", () => {
+            const edge = {
+                query_operation: {
+                    server: "https://google.com/",
+                    path: "/query"
+                },
+                association: {
+                    input_type: ['Pathway', 'SomethingElse', '{{ SpecialInput }}'],
+                    output_type: 'Gene',
+                    predicate: 'related_to'
+                },
+                input: {
+                    ids: ['123', '456'],
+                    SpecialInput: "TestSuccess"
+                }
+            }
+            const builder = new qb(edge);
+            const res = builder._getRequestBody(edge, edge.input);
+            expect(res).toEqual({
+                message: {
+                    query_graph: {
+                    nodes: {
+                        n0: {
+                        ids: ['123', '456'],
+                        categories: ['biolink:Pathway', 'biolink:SomethingElse', 'biolink:TestSuccess'],
+                        },
+                        n1: {
+                        categories: ['biolink:Gene'],
+                        },
+                    },
+                    edges: {
+                        e01: {
+                        subject: "n0",
+                        object: "n1",
+                        predicates: ['biolink:related_to'],
+                        },
+                    },
+                    },
+                },
+            });
+        })
+    })
+})